David Twomey

I spoke too soon. The text was not changed. The original text contained many instances of the gene correctly written and one typo. Kazu did not pick up the correctly...

Thank you, i will try that. Since mostly i am trying to identify genes and diseases in abstracts, missing out on a gene associated with an abstract is a big...

I understand that changing the behaviour of the AbbreviationFinder will make this better but make other things worse. I like your last suggestion though. If i did want to turn...

Here is another example where it doesn't do a great job finding PCSK9 as a gene. It does tag it as a gene but it doesn't entity link it. Is...

Let me know if i understand this. The Abbreviation finder sees the text "Proprotein convertase subtilisin/kexin type 9 (PCSK9)". It assumes PCSK9 is an abbreviation for Proprotein convertase subtilisin/kexin type...

btw: i did confirm that over-riding 'PCSK9' in AbbreviationFinder fixes this so it does confirm the issue. PCSK9,100,gene,['PCSK9'],['ENSEMBL'],['ENSG00000169174'],"{Mapping(default_label='PCSK9', source='ENSEMBL', parser_name='OPENTARGETS_TARGET', idx='ENSG00000169174', string_match_strategy='ExactMatchMappingStrategy', string_match_confidence=, disambiguation_confidence=None, disambiguation_strategy='disambiguation_not_required', xref_source_parser_name=None, metadata={'dbXRefs': [], 'approvedName': 'proprotein...

Thank you for looking in to this

Sounds good. Do you think they could quickly double check that all the HGNC approved full gene names are there? I'm sure PCSK9 and CFIm25 are not the only instances...

It's also interesting that this issue is not on the BERN2 server. But they probably don't use AbbreviationFInder and they combine protein and gene. Just curious

Hi Elliot, one more thing related to AbbreviationFinder. In that same text above, it comes across VLP in this sentence first "To do this we will use a virus-like particle...